r-ancombc: fix depends

BioArchLinux/r-ancombc/PKGBUILD

@@ -1,45 +1,49 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ANCOMBC
-_pkgver=1.6.2
+_pkgver=1.6.3
 pkgname=r-${_pkgname,,}
-pkgver=1.6.2
-pkgrel=2
-pkgdesc='Analysis of compositions of microbiomes with bias correction'
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='Microbiome differential abudance and correlation analyses with bias correction'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
   r
+  r-cvxr
   r-desctools
   r-doparallel
   r-dorng
   r-dplyr
+  r-emmeans
   r-energy
   r-foreach
   r-hmisc
+  r-lmertest
   r-magrittr
-  r-microbiome
+  r-mia
   r-nloptr
-  r-phyloseq
   r-rdpack
   r-rlang
+  r-rngtools
+  r-s4vectors
+  r-singlecellexperiment
+  r-summarizedexperiment
   r-tibble
   r-tidyr
 )
 optdepends=(
-  r-corrplot
+  r-caret
   r-dt
-  r-ggforce
   r-knitr
-  r-limma
-  r-qwraps2
+  r-microbiome
   r-rmarkdown
   r-testthat
   r-tidyverse
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5bb1cfb8b6828cd18c85d51cd2ef9d63d1a7e74eb0917aff73a6ebf94f2311b5')
+sha256sums=('32d79daf0d76f66966e6794f7763508bd873a00ab3ddb31972affd1047706b8c')
 
 build() {
   R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"

BioArchLinux/r-ancombc/lilac.yaml

@@ -3,19 +3,25 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+  - r-cvxr
   - r-desctools
   - r-doparallel
   - r-dorng
   - r-dplyr
+  - r-emmeans
   - r-energy
   - r-foreach
   - r-hmisc
+  - r-lmertest
   - r-magrittr
-- r-microbiome
+  - r-mia
   - r-nloptr
-- r-phyloseq
   - r-rdpack
   - r-rlang
+  - r-rngtools
+  - r-s4vectors
+  - r-singlecellexperiment
+  - r-summarizedexperiment
   - r-tibble
   - r-tidyr
 update_on:

BioArchLinux/r-cvxr/PKGBUILD

@@ -0,0 +1,49 @@
+# Maintainer: sukanka <su975853527@gmail.com>
+
+_pkgname=CVXR
+_pkgver=1.0-10
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='Disciplined Convex Optimization'
+arch=('x86_64')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('Apache')
+depends=(
+  r
+  r-bit64
+  r-ecosolver
+  r-gmp
+  r-osqp
+  r-r6
+  r-rcpp
+  r-rcppeigen
+  r-rmpfr
+  r-scs
+)
+optdepends=(
+  r-cccp
+  r-covr
+  r-gurobi
+  r-knitr
+  r-nnls
+  r-rcbc
+  r-rcplex
+  r-rglpk
+  r-rmarkdown
+  r-rmosek
+  r-slam
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('04118018ae99ab3fcffe5b5ccf2fc028ea11491d7078630f279ddc9135777432')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:

BioArchLinux/r-cvxr/lilac.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-cvxr/lilac.yaml

@@ -0,0 +1,18 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+repo_depends:
+  - r-bit64
+  - r-ecosolver
+  - r-gmp
+  - r-osqp
+  - r-r6
+  - r-rcpp
+  - r-rcppeigen
+  - r-rmpfr
+  - r-scs
+update_on:
+  - regex: CVXR_([\d._-]+).tar.gz
+    source: regex
+    url: https://cran.r-project.org/package=CVXR
+  - alias: r

BioArchLinux/r-ecosolver/PKGBUILD

@@ -0,0 +1,36 @@
+# system requirements: GNU make
+# Maintainer: sukanka <su975853527@gmail.com>
+
+_pkgname=ECOSolveR
+_pkgver=0.5.4
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='Embedded Conic Solver in R'
+arch=('x86_64')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('GPL')
+makedepends=('make')
+depends=(
+  r
+)
+optdepends=(
+  r-covr
+  r-knitr
+  r-matrix
+  r-rmarkdown
+  r-slam
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('5d7489e8176c1df3f3f1290732243429280efca4f837916e6b6faa6dc8a8e324')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:

BioArchLinux/r-ecosolver/lilac.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-ecosolver/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+update_on:
+  - regex: ECOSolveR_([\d._-]+).tar.gz
+    source: regex
+    url: https://cran.r-project.org/package=ECOSolveR
+  - alias: r

BioArchLinux/r-osqp/PKGBUILD

@@ -0,0 +1,31 @@
+# Maintainer: sukanka <su975853527@gmail.com>
+
+_pkgname=osqp
+_pkgver=0.6.0.6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc="Quadratic Programming Solver using the 'OSQP' Library"
+arch=('x86_64')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('Apache')
+depends=(
+  r
+  r-r6
+  r-rcpp
+)
+optdepends=(
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('853f431b96d6097fd679adb84e288e159d60bf2f0b0d6ddc06ff7acef44ec6e0')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:

BioArchLinux/r-osqp/lilac.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-osqp/lilac.yaml

@@ -0,0 +1,11 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+repo_depends:
+  - r-r6
+  - r-rcpp
+update_on:
+  - regex: osqp_([\d._-]+).tar.gz
+    source: regex
+    url: https://cran.r-project.org/package=osqp
+  - alias: r

BioArchLinux/r-scs/PKGBUILD

@@ -0,0 +1,32 @@
+# system requirements: GNU Make
+# Maintainer: sukanka <su975853527@gmail.com>
+
+_pkgname=scs
+_pkgver=3.0-1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='Splitting Conic Solver'
+arch=('x86_64')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('GPL')
+makedepends=('make')
+depends=(
+  r
+)
+optdepends=(
+  r-slam
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('d6881eeec7282f8bfbf60847327786e7f90299e4b8c0b084d8bd11fec7705913')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:

BioArchLinux/r-scs/lilac.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-scs/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+update_on:
+  - regex: scs_([\d._-]+).tar.gz
+    source: regex
+    url: https://cran.r-project.org/package=scs
+  - alias: r